Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Graded Response Model Framework for Questionnaires With Uniform Response Formats.

ABSTRACT: Questionnaires with uniform-ordered categorical response formats are widely applied in psychology. Muraki proposed a modified graded response model accounting for the items' uniform response formats by assuming identical threshold parameters defining the category boundaries for all items. What is not well known is that there is a set of closely related models, which similarly assume identical thresholds. The present article gives a framework illustrating the differences between these models and their utility for understanding questionnaire responses in detail. The models are explained as constrained cases of a one-dimensional factor model for ordered categorical data. Furthermore, the authors show that the models can be written and fitted as structural equation models, which allows for a very flexible and general purpose use. Instructions on implementing the models in Mplus and SAS PROC NLMIXED are given.

SUBMITTER: Lubbe D

PROVIDER: S-EPMC6512163 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Graded Response Model Framework for Questionnaires With Uniform Response Formats.

Lubbe Dirk D Schuster Christof C

Applied psychological measurement 20180801 4

Questionnaires with uniform-ordered categorical response formats are widely applied in psychology. Muraki proposed a modified graded response model accounting for the items' uniform response formats by assuming identical threshold parameters defining the category boundaries for all items. What is not well known is that there is a set of closely related models, which similarly assume identical thresholds. The present article gives a framework illustrating the differences between these models and ...[more]

PMID: 31156281

Similar Datasets

Uniform optimal framework for integrative next-gen sequence analysis

Project description:Here, we have collapsed multiple analysis problems into two coherent categories, signal detection and signal estimation and adapted linear-optimal solutions from signal processing theory. Our algorithms for detection (DFilter) and estimation (EFilter) extend naturally to integration of multiple datasets. In benchmarking tests, DFilter outperformed assay-specific algorithms at identifying promoters from histone ChIP-seq, binding sites from transcription factor (TF) ChIP-seq and open chromatin regions from DNase- and FAIRE-seq data. EFilter similarly outperformed an existing method for predicting mRNA levels from histone ChIP-seq data (Spearman correlation: 0.81 - 0.89). We performed H3K4me3 and H3K36me3 ChIP-seq on e11.5 mouse forebrain and used DFilter and EFilter to predict promoters and developmental gene expression, uncovering plausible gene targets for SNPs associated with neurodevelopmental disorders. Generated two histone modifiction ChiP-seq in developing embryo mouse forebrain and using them for making bioligical inferences

2013-06-10 | E-GEOD-34073 | biostudies-arrayexpress

A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

Project description:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.

| S-EPMC1681455 | biostudies-literature

Uniform optimal framework for integrative next-gen sequence analysis

2013-06-10 | GSE34073 | GEO

A Bayesian Random Block Item Response Theory Model for Forced-Choice Formats.

Project description:Based on the framework of testlet models, the current study suggests the Bayesian random block item response theory (BRB IRT) model to fit forced-choice formats where an item block is composed of three or more items. To account for local dependence among items within a block, the BRB IRT model incorporated a random block effect into the response function and used a Markov Chain Monte Carlo procedure for simultaneous estimation of item and trait parameters. The simulation results demonstrated that the BRB IRT model performed well for the estimation of item and trait parameters and for screening those with relatively low scores on target traits. As found in the literature, the composition of item blocks was crucial for model performance; negatively keyed items were required for item blocks. The empirical application showed the performance of the BRB IRT model was equivalent to that of the Thurstonian IRT model. The potential advantage of the BRB IRT model as a base for more complex measurement models was also demonstrated by incorporating gender as a covariate into the BRB IRT model to explain response probabilities. Recommendations for the adoption of forced-choice formats were provided along with the discussion about using negatively keyed items.

| S-EPMC7221495 | biostudies-literature

SCIFIO: an extensible framework to support scientific image formats.

Project description:No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation.SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment.SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

| S-EPMC5142403 | biostudies-other

The Monotonic Polynomial Graded Response Model: Implementation and a Comparative Study.

Project description:We present a monotonic polynomial graded response (GRMP) model that subsumes the unidimensional graded response model for ordered categorical responses and results in flexible category response functions. We suggest improvements in the parameterization of the polynomial underlying similar models, expand upon an underlying response variable derivation of the model, and in lieu of an overall discrimination parameter we propose an index to aid in interpreting the strength of relationship between the latent variable and underlying item responses. In applications, the GRMP is compared to two approaches: (a) a previously developed monotonic polynomial generalized partial credit (GPCMP) model; and (b) logistic and probit variants of the heteroscedastic graded response (HGR) model that we estimate using maximum marginal likelihood with the expectation-maximization algorithm. Results suggest that the GRMP can fit real data better than the GPCMP and the probit variant of the HGR, but is slightly outperformed by the logistic HGR. Two simulation studies compared the ability of the GRMP and logistic HGR to recover category response functions. While the GRMP showed some ability to recover HGR response functions and those based on kernel smoothing, the HGR was more specific in the types of response functions it could recover. In general, the GRMP and HGR make different assumptions regarding the underlying response variables, and can result in different category response function shapes.

| S-EPMC7383691 | biostudies-literature

Using graded response model for the prediction of prostate cancer risk.

Project description:Disease risk-associated single nucleotide polymorphisms (SNPs) identified from genome-wide association studies (GWAS) have the potential to be used for disease risk prediction. An important feature of these risk-associated SNPs is their weak individual effect but stronger cumulative effect on disease risk. To date, a stable summary estimate of the joint effect of genetic variants on disease risk prediction is not available. In this study, we propose to use the graded response model (GRM), which is based on the item response theory, for estimating the individual risk that is associated with a set of SNPs. We compare the GRM with a recently proposed risk prediction model called cumulative relative risk (CRR). Thirty-three prostate cancer risk-associated SNPs were originally discovered in GWAS by December 2009. These SNPs were used to evaluate the performance of GRM and CRR for predicting prostate cancer risk in three GWAS populations, including populations from Sweden, Johns Hopkins Hospital, and the National Cancer Institute Cancer Genetic Markers of Susceptibility study. Computational results show that the risk prediction estimates of GRM, compared to CRR, are less biased and more stable.

| S-EPMC3734950 | biostudies-literature

Kronos scRT: a uniform framework for single-cell replication timing analysis

Project description:Mammalian genomes are replicated in a cell-type specific order and in coordination with transcription and chromatin organization. Although the field of replication is also entering the singlecell era, current studies require cell sorting, individual cell processing and have yielded a limited number (<100) of cells. Here, we have developed Kronos scRT (https://github.com/CL-CHEN-Lab/Kronos_scRT), a software for single-cell Replication Timing (scRT) analysis. Kronos scRT does not require a specific platform nor cell sorting, allowing the investigation of large datasets obtained from asynchronous cells. Analysis of published available data and droplet-based scWGS data generated in the current study, allows exploitation of scRT data from thousands of cells for different mouse and human cell lines. Our results demonstrate that, although most cells replicate within a close timing range for a given genomic region, replication can also occur stochastically throughout S phase. Altogether, Kronos scRT allows investigating the RT program at a single-cell resolution for both homogeneous and heterogeneous cell populations in a fast and comprehensive manner.

2022-03-29 | GSE186173 | GEO

Optimal Examination Sites for Periodontal Disease Evaluation: Applying the Item Response Theory Graded Response Model.

Project description:Periodontal examination data have a complex structure. For epidemiological studies, mass screenings, and public health use, a simple index that represents the periodontal condition is necessary. Periodontal indices for partial examination of selected teeth have been developed. However, the selected teeth vary between indices, and a justification for the selection of examination teeth has not been presented. We applied a graded response model based on the item response theory to select optimal examination teeth and sites that represent periodontal conditions. Data were obtained from 254 patients who participated in a multicenter follow-up study. Baseline data were obtained from initial follow-up. Optimal examination sites were selected using item information calculated by graded response modeling. Twelve sites-maxillary 2nd premolar (palatal-medial), 1st premolar (palatal-distal), canine (palatal-medial), lateral incisor (palatal-central), central incisor (palatal-distal) and mandibular 1st premolar (lingual, medial)-were selected. Mean values for clinical attachment level, probing pocket depth, and bleeding on probing by full mouth examinations were used for objective variables. Measuring the clinical parameters of these sites can predict the results of full mouth examination. For calculating the periodontal index by partial oral examination, a justification for the selection of examination sites is essential. This study presents an evidence-based partial examination methodology and its modeling.

| S-EPMC7700480 | biostudies-literature

The Indecision Model of Psychophysical Performance in Dual-Presentation Tasks: Parameter Estimation and Comparative Analysis of Response Formats.

Project description:Psychophysical data from dual-presentation tasks are often collected with the two-alternative forced-choice (2AFC) response format, asking observers to guess when uncertain. For an analytical description of performance, psychometric functions are then fitted to data aggregated across the two orders/positions in which stimuli were presented. Yet, order effects make aggregated data uninterpretable, and the bias with which observers guess when uncertain precludes separating sensory from decisional components of performance. A ternary response format in which observers are also allowed to report indecision should fix these problems, but a comparative analysis with the 2AFC format has never been conducted. In addition, fitting ternary data separated by presentation order poses serious challenges. To address these issues, we extended the indecision model of psychophysical performance to accommodate the ternary, 2AFC, and same-different response formats in detection and discrimination tasks. Relevant issues for parameter estimation are also discussed along with simulation results that document the superiority of the ternary format. These advantages are demonstrated by fitting the indecision model to published detection and discrimination data collected with the ternary, 2AFC, or same-different formats, which had been analyzed differently in the sources. These examples also show that 2AFC data are unsuitable for testing certain types of hypotheses. matlab and R routines written for our purposes are available as Supplementary Material, which should help spread the use of the ternary format for dependable collection and interpretation of psychophysical data.

| S-EPMC5506217 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data